average_chr_signal: Average signal genome-wide and on each chromosome

In hochwagenlab/hwglabr2: Collection of R functions used in the Hochwagen Lab

Average signal genome-wide and on each chromosome

Description

Computes average signal (in the score GRanges metadata column) genome-wide and on each chromosome (each individual sequence determined by seqnames).

Usage

average_chr_signal(
  gr,
  remove_cen = FALSE,
  genome,
  cen_region_length = 50000,
  mean_norm = FALSE,
  order_chrs = FALSE
)

Arguments

gr	Input signal track data as a GRanges object (see ?"GRanges-class" for more details). To load wiggle and bedGraph data run import_wiggle and import_bedGraph, respectively. No default.
remove_cen	Logical indicating whether to remove regions around centromeres. Defaults to FALSE.
genome	Character string indicating reference genome used to align the data. Must be provided when remove_cen = TRUE, in order to load appropriate centromere data, or order_chrs = TRUE, in order to load chromosome length data. Accepts one of the following strings: "SK1Yue" "sacCer3" "SK1" No default.
cen_region_length	Integer indicating the length (in bp) of the region to remove (centered on the centromere of each chromosome). Defaults to 50'000 bp.
mean_norm	Logical indicating whether to normalize by average genome-wide score. This adds two columns to the dataframe (first element of the output list): mean ratio (avrg_signal_mean_ratio) and mean-subtracted (avrg_signal_mean_subtracted). Defaults to FALSE.
order_chrs	Logical indicating whether to order rows by chromosome length (in increasing order). Defaults to FALSE.

Value

List with two elements:

1. seq_avrg Average score on each sequence (dataframe)

2. genome_avrg Average score genome-wide (named vector)

Examples

## Not run: 
average_chr_signal(GRanges_object)

average_chr_signal(anti_Rec8, remove_cen=TRUE, mean_norm=TRUE, order_chrs=TRUE)

average_chr_signal(anti_Rec8, remove_cen=TRUE, genome = 'SK1Yue',
                   cen_region_length=40000, mean_norm=TRUE, order_chrs=TRUE)

## End(Not run)

hochwagenlab/hwglabr2 documentation built on Nov. 12, 2022, 7:27 p.m.